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Supplementary Information
A Holistic View into the Gallic Acid-induced Attenuation in Colitis
Based on the Microbiome-Metabolomics Analysis
Yuan Lia†, Zhiyong Xieb, c†, Tingting Gaoa, Lin Lia, Yongda Chena, Dan Xiaob, Wen
Liub, Baorong Zoub, Biyu Lua, Xing Tiand, Bo Hand, Yaping Guoe, Shaobao Zhangb,
Lei Linb, Mengxia Wanga, Pei Lia, Qiongfeng Liaoa*
a. School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine,
Guangzhou, China.
b. School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University,
Guangzhou, 510006, China
c. Guangdong Provincial Key Laboratory of New Drug Design and Evaluation,
Guangzhou, China
d. School of Pharmacy, Xinjiang Shihezi University, Xinjiang, 832002, China
e. The first affiliated hospital, School of medicine, Xinjiang Shihezi university,
Xinjiang, 832002, China.
† These authors contributed equally to this work and should be considered co-first
authors.
*Corresponding authors:
Qiongfeng Liao
Tel./Fax: +86 20 3935 8081E-mail: [email protected]
Electronic Supplementary Material (ESI) for Food & Function.This journal is © The Royal Society of Chemistry 2019
Figure 1. LDA score plot
Figure 2. PCA score plot based on PICRUSt analysis
Figure 3. PCA scores plots of 1H NMR data of feces and urine
Table 1. Relative abundance of major bacterial taxa among different groups
Table 2. 1H NMR data of metabolites in rat feces
Table 3. 1H NMR data of metabolites in rat urine
Table 4. Screened metabolites with significant difference in fold change (FC)
value in feces samples
Table 5. Screened metabolites with significant difference in fold change (FC)
value in urine samples
Figure 1. LDA score plot
Figure 2. PCA score plot based on PICRUSt analysis
PICRUSt analysis shows the relative abundance of predicted microbial genes related to metabolism among groups based on Welch’s t test.
Figure 3. PCA scores plots of 1H NMR data of feces and urine
Table 1. Relative abundance of major bacterial taxa among different groupsPhylum Family Genus Relative abundance(%)
Control DSS DSS±GACorynebacteriaceae Corynebacterium 0.19±0.17 0.00±0.00## 0.04±0.05
Micrococcaceae Rothia 0.01±0.00 0.01±0.01 0.01±0.01Bifidobacteriaceae Bifidobacterium 0.03±0.06 0.02±0.05 0.03±0.06Actinobacteria
Coriobacteriaceae Adlercreutzia 0.01±0.00 0.00±.0.00## 0.01±0.01
Bacteroidaceae Bacteroides 0.77±0.36 5.54±4.57## 19.70±9.77*##
Porphyromonadaceae Parabacteroides 0.19±0.07 2.04±2.54## 1.33±1.39#
Prevotellaceae Prevotella 31.82±9.06 3.33±5.58## 0.00±0.00*##
Rikenellaceae AF12 0.05±0.04 0.00±0.00## 0.00±0.00##
S24-7 g_ 25.84±3.54 21.2±3.13 25.31±13.00Butyricimonas 0.03±0.03 0.04±0.04 0.00±0.00*##
[Odoribacteraceae]Odoribacter 0.01±0.01 0.01±0.01 0.00±0.00
[Paraprevotellaceae] Paraprevotella 4.84±5.27 5.39±5.38 3.03±1.42
Bacteroidetes
[Paraprevotellaceae] [Prevotella] 2.23±2.12 7.66±2.46## 9.68±8.20Deferribacteres Deferribacteraceae Mucispirillum 0.01±0.01 0.01±0.01 0.00±0.00
Lactobacillaceae Lactobacillus 4.40±2.02 0.61±0.49## 2.10±1.78
Streptococcaceae Lactococcus 0.00±0.00 0.02±0.02## 0.00±0.00**
Turicibacteraceae Turicibacter 0.06±0.10 0.69±0.63## 0.13±0.13*
Candidatus Arthromitus 0.00±0.00 0.00±0.00 0.01±0.01Clostridiaceae Clostridium 0.08±0.07 0.26±0.31 0.04±0.06Dehalobacteriaceae Dehalobacterium 0.04±0.02 0.02±0.02 0.10.±0.08
Blautia 0.05±0.11 0.26±.32 0.10±0.14Coprococcus 0.20±0.32 0.35±0.16 0.57±0.44
Dorea 0.04±0.02 0.20±0.19## 0.10±0.13
Firmicutes
Lachnospiraceae
Lachnospira 0.01±0.01 0.00±0.00 0.04±0.07
Roseburia 0.03±0.03 0.09±0.22 0.10±0.17[Ruminococcus] 0.19±0.15 0.35±0.47 0.13±0.08
Peptococcaceae rc4-4 0.02±0.02 0.13±0.03## 0.37±0.25*##
Oscillospira 2.33±1.10 5.67±4.32 5.01±2.89Ruminococcaceae Ruminococcus 4.59±1.34 2.75±0.85## 3.50±1.63
Veillonellaceae Phascolarctobacterium 0.30±0.72 1.35±0.80# 0.98±1.39
Allobaculum 0.01±0.00 0.44±0.35## 0.22±0.44##Erysipelotrichaceae
p-75-a5 0.01±0.01 0.01±0.01 0.00±0.00Alcaligenaceae Sutterella 0.42±0.17 2.70±1.49## 0.78±0.59*
Bilophila 0.02±0.02 0.00±.0.00# 0.00±0.00##Desulfovibrionaceae
Desulfovibrio 0.09±0.12 0.10±0.07 0.03±0.05*
Helicobacteraceae Flexispira 0.24±0.24 1.09±2.03 0.50±0.47
Proteobacteria
Enterobacteriaceae Proteus 0.00±0.00 0.01±0.01 0.01±0.01Spirochaetes Spirochaetaceae Treponema 4.18±5.25 0.26±0.42# 0.00±0.00##
Tenericutes Mycoplasmataceae Mycoplasma 0.02±0.02 0.04±0.03 0.06±0.05Verrucomicrobia Verrucomicrobiaceae Akkermansia 1.22±2.68 0.00±0.00# 0.00±0.00#
The data are expressed as the mean ± SD (n=6). p vales are calculated with Mann-Whitney U test. (vs. DSS :* P<0.05,**P<0.01;vs. control :# P<0.05,##P<0.01)
Table 2. 1H NMR data of metabolites in rat feces
Number Metabolites δ 1H (ppm)1 2-Hydroxyisobutyrate 1.35(s)2 3-Methyl-2-oxovalerate 0.899(t), 1.093(d), 1.438(m), 1.662(m)1.685, 2.928(m), 1.924(s) 3 Alanine 1.484(d), 3.780(q)4 Acetate 1.924(s) 5 Asparagine 2.862(dd), 2.962(m), 3.993(dd)6 Aspartate 2.666(dd), 2.805(dd), 3.898(dd)7 Choline 3.191(s), 3.504(m), 4.085(m)8 Creatine 3.045(s), 3.927(s)9 Dimethylamine 2.719(s)10 Formate 8.460(s)11 Fumarate 6.525(s) 12 Glycerol 3.551(dd), 3.634(m), 3.767(m) 3.76813 Glycine 3.567(s) 14 Histidines 3.144(dd), 3.249(dd), 4.003(dd), 7.093(s), 7.844(s)15 Isoleucine 0.936(t), 0.993 (d), 1.249(m), 1.452(m), 1.971(m), 3.655(d) 16 Lactate 1.335(d), 4.125(q)17 Leucine 0.925(d), 0.935(s), 1.703(m), 3.724 (d) 18 Methylamine 2.613(s)19 Pyruvate 2.374(s)20 Succinate 2.410(s)21 Threonine 1.335(d), 3.578(d), 4.269(m)22 Xanthine 7.909(s)23 α-Glucose 3.418 (m), 3.547 (m), 3.726(m), 3.742(m), 3.772(m), 3.870 (m), 5.210(d)24 1,3-dihydroxyacetone 3.573(s), 4.42(s)
25 2-Ketoisovalerate 1.127(d), 3.027(m)26 3-Methyl-2-ketovalerate 0.888(t;7.4), 1.102(d;7.0), 1.461(m), 1.727(m), 2.939(m)27 3-hydroxyphenylacetate 3.481(s), 6.757(m), 6.807(d), 6.906(dd), 7.245 (t)28 Adenine 8.196(s), 8.213(s)29 Butyrate 0.899(t), 1.553(m), 2.150(t)30 Cadaverine 1.484(d), 1.727(m), 3.022(t)31 DCA 6.859(d)32 desaminotyrosine 3.817(d)33 Ethanolamine 3.134(d), 7.850(d;7.6)34 Glutarate 1.775(overlap), 2.181(t)35 Hypoxanthine 8.196(s), 8.216(s)36 Imidazole 7.327(s), 8.297(s)37 Isocaproate 0.882(d), 1.449(m), 1.484 (d), 2.189 (t)38 Malonate 3.112(s)39 Methanol 3.366(s)40 Methionine 2.142 (s), 2.169(m), 2.648(t), 3.853(m)41 Methylsuccinate 1.104(d), 2.135 (d), 2.635 (m)42 N-acetyl-glycoprotein 2.03(s)43 NAG 2.042(s), 2.065(s)44 Phenylacetate 3.542(s), 7.317(m), 7.375(m)45 Propionate 1.060(t), 2.187(q), 2.374(s)46 Sarcosine 2.705(s), 3.598(s)47 Taurochenodeoxycholate 0.957, 0.672(s), 0.965(s)48 TCA 0.67(s)49 Trimethylamine 2.871(s)50 Tyrosine 3.068(d), 3.140(dd), 3.941(d), 6.907(m), 7.196 (d/m51 Uracil 5.807(d), 7.542(d) 52 Urocanate 6.40(d), 7.318(d), 7.433(s), 7.885(s)53 Valerate 0.899(t), 1.309(m), 2.178(t)
54 Valine 0.972(d), 1.013(d), 2.275(m), 3.617(d), 7.909(s)55 α-arabinose 3.849(dd), 3.906(m), 3.993(t), 4.023(d), 5.242 (d)56 α-galactose 3.64(dd), 4.08(m), 4.58(d), 5.274 (d)57 α-ketoisocaproate 0.920 (s), 2.054(m), 2.616(d)58 α-ketoisovalerate 1.127(d), 3.022(m)59 α-xylose 3.545(dd), 3.630(m), 3.670 (t), 5.203(d)60 β-arabinose 3.525(dd), 3.670 (t), 3.856(dd), 3.945(m), 4.523(d)61 β-L-Fucose 1.251(d:6.5), 3.452(m), 3.645 (m), 3.804 (m) , 4.561 (d;7.9)62 β-xylose 3.23(dd), 3.46(t), 3.63(m), 3.932(dd), 4.570(d)
Abbreviation: TCA, Taurocholic acid; DCA, Deoxycholic acid; NAG, N-Acetyl group contained glycoprotein
Table 3. 1H NMR data of metabolites in rat urine
1H NMR Data of Metabolites in Rat Urine
Number Metabolites δ 1H (ppm)1 1-Methylnicotinamide 4.476(s),8.181(t),8.894(d),8.960(d),9.272(s)2 2-Hydroxy-3-methylvalerate 0.8(t),0.93(d),1.15(m),1.35(m),1.75(m),3.87(d)3 2PY 6.67(d), 7.97(dd), 8.34(d), 3.65(s)4 3-Hydeoxyphenylacetate 3.490(s),6.794(m),6.872(m or ov),7.258(tr or ov)5 3-Hydroxyisovalerate 1.275(s), 2.357(s)6 4-Hydroxyhippurate 3.978(s),6.976(d),7.765(d)7 4-hydroxyphenylacetate 6.87(d)8 4PY 6.70(d),7.83(dd) ,8.56(d) ,3.90(s)9 4-Pyridoxate 2.429(s),7.834(s)10 Acetamide 1.99(s) 11 Acetoacetate 2.266(s),3.434(s)12 Acetone 2.229(s)13 Acetylcarnitine 2.159(s), 2.504(m), 2.631(m), 3.202(s), 3.621(d), 3.829(dd), 14 Allantoin 5.38(s), 6.02(s), 7.27(s), 8.01(s)15 Betaine 3.273(s),3.927(s)16 Carnitine 2.41(t),3.230(s),3.405(m),4.554(m)17 cis-aconitate 3.123(s/d),5.711(t)18 Creatinine 3.043(s),4.052(s)19 Dimethyl sulfone 3.145(s)20 Galactarate 3.95(s), 4.26(s)21 Galactonate 4.26(s)22 Glycerate 3-phosphate 4.22(m), 4.06(d), 3.84(d)
23 Glycolate 3.932(s)24 Guanidoacetate 3.801(s)25 Guanine 7.69(s)26 Hippurate 3.975(d), 7.553(t), 7.642(t), 7.837(d), 8.508(s)27 Hypotaurine 3.36(t)28 Indole-3-acetate 3.681 (s), 7.161 (t), 7.216 (t), 7.507 (d), 7.635(d)29 Isobutyrate 1.053 (d), 2.382(m)30 Isopropanol 1.146 (d), 4.028(m)31 Isovalerate 0.895(d), 1.929(m), 2.049(d)32 Isovalerylglycine 0.925(d), 1.994(m), 2.166(d),3.746(d)33 Ketoleucine 0.944 (d), 2.100 (m), 2.617(d)
34 Lactose 3.276 (t), 3.507 (m), 3.604 (m), 3.710 (m), 3.768 (m), 3.847 (m), 3.936 (m), 4.455 (d), 4.660 (d), 5.211(d)
35 Methylguanidine 2.828 (s), 3.356(s)36 N, N-dimethylglycine 2.925 (s), 3.712(s)37 N6, N6, N6-trimethyllysine 3.109(s)38 N-acetylglutamate 4.13(t), 1.83(m), 2.27(t), 2.04(s)39 N-Acetylglycine 2.044 (s), 3.763 (d), 7.997(s)40 N-methylhydantoin 2.91(s), 4.08(s)41 N-Nitrosodimethylamine 3.162 (s), 3.802(s)42 N-Phenylacetylglycine 3.67(s), 3.74(d), 7.98(s)43 O-Acetylcholine 2.143 (s), 3.202 (s), 3.711 (t/m), 4.529(m)44 Oxypurinol 8.209(s)45 Pantothenate 0.94(s), 0.90(s), 3.52(s), 3.40(s), 4.00(s), 3.45(t), 2.43(t) 46 p-cresol 2.253 (s), 6.817 (d), 7.130(d)47 p-Cresol glucuronide 2.299 (s), 7.055 (m), 7.237(m)48 p-cresol sulfate 2.347(s), 7.217 (d), 7.293(s,d,d)49 Phenylacetylglycine 3.680 (s), 3.746 (d), 7.365 (t), 7.425(t)
50 Phosphorylcholine 3.203 (s), 3.671 (t), 4.190(dd)51 Propylene glycol 1.14(d), 3.44(dd), 3.54(dd), 3.88(m)52 Succinimide 2.78(s)53 Thiamine 9.42(s), 8.04(s), 5.45(s), 3.89(t), 3.18(t), 2.56(s), 2.49(s)54 Trans-Aconitate 3.435 (s), 6.571(s)55 Trigonelline 4.438 (s), 8.084 (t), 8.837 (t/d), 9.122(s)56 TMAO 3.266(s)57 β-Glucose 3.243 (t), 3.478 (m), 3.492 (m), 3.864 (m), 3.927 (s), 4.660(d)58 4-hydroxyphenylacetate 3.45(s), 6.87(d), 7.16(d)59 3-hydroxyisobutyrate 1.06(d), 2.48(m), 3.52(m), 3.71(m)60 GPC 3.24(s), 3.69(m), 4.33(m)61 NAG 2.04(s) 62 PC 3.22(s), 3.60(m), 4.17(m)63 Dimethylglycine 2.92(s), 3.72(s)64 2-Hydroxyisobutyrate 1.35(s)65 3-Methyl-2-oxovalerate 0.899(t), 1.093(d), 1.438(m), 1.662(m), 2.928(m)66 Alanine 1.489(d), 3.780(q) 67 Acetate 1.927(s)68 Asparagine 2.862(dd), 2.962(m), 3.995(dd)69 Choline 3.191(s), 3.504(t/m), 4.085(m)70 Citrulline 1.558(m), 1.865(m), 3.124(dd), 3.743(t)71 Creatine 3.028/3.047(s), 3.926(s)72 DMA 2.719(s)73 Formate 8.467(s)74 Fumarate 6.524(s)75 Glycine 3.566(s)76 Isoleucine 0.936(t), 0.995(d), 1.249(m), 1.452(m), 1.971(m), 3.655(d)77 Lactate 1.331(d), 4.115(q)
78 Leucine 0.925(d), 0.936(s/d), 1.703(m), 3.725(d)79 Pyruvate 2.373(s)80 p-Hydroxyphenylacetate 3.445(s), 6.865 (d), 7.169(d)81 Succinate 2.413(s)82 Taurine 3.243(t), 3.435(t)83 Threonine 1.330(d), 3.579(d), 4.269(m)84 Xanthine 7.909(s)
Abbreviation: 2PY, N'-methyl-2-pyridone-5-carboxamide; 4PY, N'-methyl-4-pyridone-3-carboxamide; TMAO, Trimethylamine-N-oxide; GPC, Glycerophosphocholine; NAG, N-Acetyl group contained glycoprotein; PC, Phosphorylcholine; DMA, Dimethylamine;
Table 4. Screened metabolites with significant difference in fold change (FC) value in feces samples.
DSS / Control DSS+GA / Control DSS+GA / DSSNumber Metabolites
FC p value Trend FC p value Trend FC p value Trend1 Valerate 2.618 0.007 ↑** 0.450 0.012 ↓*2 Butyrate 1.987 0.014 ↑* 0.532 0.013 ↓*3 Glutarate 1.740 0.01 ↑* 0.578 0.012 ↓*4 Taurochenodeoxycholate 1.655 0.009 ↑**5 Glycine 1.563 0.005 ↑** 1.544 0.002 ↑**6 Methionine 1.517 0.006 ↑** 0.712 0.013 ↓*7 3-Methyl-2-ketovalerate 1.515 0.015 ↑* 0.640 0.013 ↓*8 Propionate 1.509 0.014 ↑* 0.635 0.007 ↓**9 Methylsuccinate 1.503 0.014 ↑* 0.699 0.024 ↓*10 3-Methyl-2-oxovalerate 1.465 0.029 ↑* 0.627 0.013 ↓*11 Acetate 1.465 0.027 ↑* 0.688 0.030 ↓*12 Dimethylamine 0.809 0.002 ↓**13 Adenine 0.800 0.046 ↓*14 Uracil 0.776 0.025 ↓*15 Fumarate 0.739 <0.001 ↓*** 0.733 0.003 ↓**16 Deoxycholic acid 0.637 <0.001 ↓*** 0.703 0.002 ↓**17 Asparagine 1.264 <0.001 ↑***18 Desaminotyrosine 1.261 0.005 ↑** 1.212 0.032 ↓*19 Alpha-arabinose 1.208 0.005 ↑**20 Xanthine 0.750 <0.001 ↓***21 α-galactose 1.234 <0.001 ↑***22 β-xylose 1.280 0.003 ↑**23 β-arabinose 1.249 0.004 ↑**24 α-xylose 1.240 0.008 ↑**
25 Isocaproate 0.782 0.018 ↓**p<0.05; **p<0.01, ***p<0.001
Table 5. Screened metabolites with significant difference in fold change (FC) value in urine samplesDSS / Control DSS+GA / Control DSS+GA / DSS
Number MetabolitesFC p value Trend FC p value Trend FC p value Trend
1 Oxypurinol 0.337 <0.001 ↓*** 2.771 <0.001 ↑***2 Xanthine 0.588 <0.001 ↓*** 1.691 <0.001 ↑***3 4-Hydroxyhippurate 0.714 <0.001 ↓*** 0.648 <0.001 ↓***4 Hippurate 0.719 <0.001 ↓*** 0.650 <0.001 ↓***5 cis-aconitate 0.792 <0.001 ↓***6 Galactarate 0.815 <0.001 ↓***7 Isovalerate 1.421 <0.001 ↑*** 1.280 <0.001 ↑***8 Acetoacetate 0.723 0.045 ↓*9 Succinate 1.605 0.021 ↑*10 Fumarate 0.806 0.020 ↓*11 Isopropanol 0.707 0.016 ↓* 0.742 0.033 ↓**12 Acetate 2.154 0.011 ↑* 1.316 0.002 ↑**13 Taurine 0.646 0.008 ↓**14 trans-Aconitate 0.506 0.008 ↓**15 Trigonelline 0.830 0.006 ↓** 1.219 0.002 ↑**16 4-Pyridoxate 0.741 0.005 ↓** 0.628 <0.001 ↓***17 2-Hydroxyisobutyrate 1.542 0.003 ↑** 1.338 <0.001 ↑***18 Formate 1.659 0.001 ↑** 0.661 0.010 ↓**19 Indole-3-acetate 0.674 <0.001 ↓***20 succinimide 1.239 <0.001 ↑***21 p-Cresol glucuronide 0.753 <0.001 ↓***22 Glycolate 0.783 <0.001 ↓***23 Asparagine 0.800 <0.001 ↓***24 Phenylacetylglycine 0.797 <0.001 ↓***
*p<0.05; **p<0.01, ***p<0.001